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Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data.

Amrita Chattopadhyay1, Chien-Yueh Lee2, Ying-Cheng Shen3

  • 1Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.

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|June 12, 2023
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Summary

This study introduces the Multi-ethnic Imputation System (MI-System), a web platform for genotype imputation in East Asian populations. MI-System enhances genetic research by providing tools for accurate imputation and reference panel customization, accessible to researchers with limited resources.

Keywords:
Beagle5.1Genotype imputationIMPUTE2IMPUTE5Taiwan biobankWeb-server

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Area of Science:

  • Genetics
  • Bioinformatics
  • Population Genomics

Background:

  • Genotype imputation is crucial for identifying causal variants in disease studies.
  • Existing imputation resources are Caucasian-centric, limiting research in other ethnic groups.
  • Accurate imputation for Asian ancestry is vital for understanding health outcomes and improving risk prediction models.

Purpose of the Study:

  • To develop a collaborative, web-based platform for genotype imputation and analysis, focusing on East Asian populations.
  • To enable researchers to perform accurate and efficient genotype imputation with minimal computational resources and bioinformatics expertise.
  • To facilitate advancements in Asian population genetics and patient-driven research for complex diseases.

Main Methods:

  • Developed the Multi-ethnic Imputation System (MI-System), an online platform accessible at https://misystem.cgm.ntu.edu.tw.
  • Integrated three established imputation pipelines: SHAPEIT2-IMPUTE2, SHAPEIT4-IMPUTE5, and Beagle5.1.
  • Incorporated standard reference panels (1000 Genomes, Hapmap3) and a novel Taiwan Biobank (TWB) reference panel tailored for Taiwanese-Chinese ancestry.

Main Results:

  • MI-System offers users a streamlined process for uploading genotype data and performing imputation.
  • The platform provides essential utility functions: creating custom reference panels, quality control, data splitting by chromosome, and genome build conversion.
  • Users can combine reference panels for more tailored imputation analyses.

Conclusions:

  • MI-System significantly lowers the barrier for conducting genotype imputation in East Asian populations.
  • The platform empowers researchers by providing accessible tools, fostering advancements in genetic research for diverse ancestries.
  • MI-System accelerates research and contributes to a better understanding of genetic factors in complex diseases, supporting patient-driven research.